Number of cases with aa genotype (a vector
corresponding to the snps).
case.Aa
Number of cases with Aa genotype.
case.AA
Number of cases with AA genotype.
control.aa
Number of controls with aa genotype.
control.Aa
Number of controls with Aa genotype.
control.AA
Number of controls with AA genotype.
replicates
This value should be set to zero for the first
analysis. Then, once the top snps have been selected, this should be
rerun with replicates>1000 for those selected snps.
statistic
"armitage" = the Armitage trend test.
"logrank" = logrank test
method
"exact" = exact likelihood function
"approximate" = approximate likelihood function
Details
The output is formatted as follows:
SNP, case.aa, case.Aa, case.AA, control.aa, control.Aa, control.AA,
Monte-Carlo p-value, p-value, non-centrality parameter (for power
calculations), modelc2-based OR, allelic OR.
Note that the non-centrality parameter and the ORs are independent of
the pvalues.